Dr. Li is interested in the research of topology structure, biological function, evolution and dynamics of the large-scale biological networks. In the past five years, he has revealed the conserved diameter of the protein-protein interaction network and found hub proteins play important roles in their robustness, developed an integrated functional annotation strategy based on gene ontology (GOfact), presented an online protein-protein interaction confidence assessment system by integrating multiple biological evidences (PRINCESS) and mined the biological knowledge from the large-scale human liver protein-protein interaction networks. And now, Dr. Li is leading his team to establish a knowledge discovery platform to integrate multiple genome-scale datasets (genomic, transcriptomic and proteomic) into network models to generate biological hypothesis for experimental validation. And they also try to diagnose disease and interpret personalized genetic information using network models.
1. Dong Li, Wanlin Liu, Zhongyang Liu, Jian Wang, Yunping Zhu, Fuchu He, PRINCESS: a PRotein INteraction Confidence Evaluation System with multiple data Sources. Molecular & Cellular Proteomics, 2008, Jun 7: 1043-1052.
2. Liu Z, Guo F, Zhang J, Wang J, Lu L, Li D*, He F*. Proteome-wide prediction of self-interacting proteins based on multiple properties. Mol Cell Proteomics. 2013 Jun;12(6):1689-700.
3. Liu W*, Li D*, Wang J, Xie H，Zhu Y, He F, Proteome-wide prediction of signal flow direction in protein interaction network based on interacting domains. Molecular & Cellular Proteomics, 2009, Sep;8(9):2063-70.
4. Guo F, Wang D, Liu Z, Lu L, Zhang W, Sun H, Zhang H, Ma J, Wu S, Li N, Jiang Y, Zhu W, Qin J, Xu P, Li D*, He F*. CAPER: a Chromosome-Assembled human Proteome browsER. J Proteome Res. 2013 Jan 4;12(1):179-86.
5. Wang, Dan; Liu, Zhongyang; Guo, Feifei; Diao, Lihong; Li, Yang; Zhang, Xinlei; Huang, Zechi; Li, Dong*; He, Fuchu*, CAPER2.0: an interactive, configurable and extensible workflow-based platform to analyze datasets from the Chromosome-centric Human Proteome Project, J Proteome Res, 2014, 13: 99-106
6. Shuai Yang , Xinlei Zhang , Hongli Diao , Feifei Guo , Dan Wang , Zhongyang Liu , Honglei Li , Junjie Zheng , Jingshan Pan , Edouard C. Nice , Dong Li* , and Fuchu He*. CAPER 3.0: a scalable cloud-based system for data-intensive analysis of Chromosome-centric Human Proteome Project datasets. J. Proteome Res., 2015, 14: 3720-8.
7. Jian Wang*, Keke Huo*, Lixin Ma*, Liujun Tang*, Dong Li*, et al., Toward an understanding of the protein interaction network of the human liver. Molecular Systems Biology, 2011 7: 536
8. Li D, Li J, Ouyang S, Wang J, et al., Protein Interaction Networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large-Scale Organization and Robustness, Proteomics, 2006, Jan, 6:456-461.
9. LI Dong, LI Jian-Qi, OUYANG Shu-Guang, WANG Jian, et al., An Integrated Strategy for Functional Analysis in Large-scale Proteomic Research by Gene Ontology, Progress in Biochemistry and Biophysics, 2005, 32: 1026 - 1029.
10. Zhongyang Liu, Feifei Guo, Jiangyong Gu, Yong Wang, Yang Li, Dan Wang, Liang Lu, Dong Li*, and Fuchu He*. Similarity-based prediction for Anatomical Therapeutic Chemical classification of drugs by integrating multiple data sources, Bioinformatics, 2015，31：1788-95
11. Liu Z, Liu Q, Sun H, Hou L, Guo H, Zhu Y, Li D*, He F*. Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs. BMC Evol Biol. 2011; May, 11(1):133.
12. Sun H *, Li D*, Wang J, Liu Z, Xie H, Zhu Y, He F, PNmerger: a Cytoscape plugin to merge biological pathways and protein interaction networks. Prog Biochem Biophys, 2009, 36: 1613-1616
13. Wanlin Liu, Dong Li*, Qijun Liu, Yunping Zhu and Fuchu He, A novel parametric approach to mine gene regulatory relationship from microarray datasets, BMC bioinformatics, 2010, 11: S15